In order to alleviate liquid water flooding in polymer electrolyte fuel cells (PEFCs), it is essential to design the optimum electrode structure on cathode side. In this study, the liquid water behavior in the cathode flow field of an operating PEFC was directly visualized using a high-resolution digital CCD camera, and the effect of perforation structure of cathode gas diffusion layer (GDL) on the liquid water transport and cell performance was investigated. The perforation holes were cut in the porous GDL by electric discharge machining or micro-driling technique. It was noted that the hydrophobic perforation holes machined by the micro-driling technique are effective in removing liquid water in the cathode GDL.